gffx 0.4.0

An ultra-fast and memory-efficient toolkit for querying GFF files, written with Rust
Documentation 
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use crate::build_index;
use anyhow::Result;
use clap::Parser;
use std::path::PathBuf;

#[derive(Parser, Debug)]
#[command(
    about = "Build index for GFF file",
    long_about = "This command builds index files for fast retrieval from a GFF file."
)]
pub struct IndexArgs {
    #[arg(short, long)]
    input: PathBuf,

    #[arg(short, long, default_value = "gene_name")]
    pub attribute: String,

    #[arg(short, long, default_value = "remark,note,comment,region,gap,assembly_gap,contig,scaffold,source")]
    pub skip_types: String,

    #[arg(short, long, default_value_t = false)]
    verbose: bool,
}

pub fn run(args: &IndexArgs) -> Result<()> {
    if args.verbose {
        println!("Indexing: {}", args.input.display());
    }

    build_index(&args.input, &args.attribute, &args.skip_types, args.verbose)?;

    if args.verbose {
        println!("Index created successfully.");
    }

    Ok(())
}